The term Molar-Incisor Hypomineralisation (MIH) is used to describe hypomineralised defects of systemic origin that affect at least one of the first permanent molars and often involves the permanent incisors. Antibiotic therapy during amelogenesis may be associated with enamel hypomineralisation. By examining children with Sickle Cell Disease (SCD), who take prophylactic antibiotics daily from birth until age five, it may be possible to determine if there is an increased prevalence of MIH in this population. The aim of this study was to determine the effect of long-term antibiotic use on the prevalence and severity of MIH in children with SCD. In a prospective cohort pilot study over a period of seven months, children aged 7-17 years, with SCD at Boston Children's Hospital (n = 18) were examined for MIH. Information regarding peri-natal concerns, incidence of illness and antibiotic use were also collected. The results were compared to a group of control patients (n = 63) for prevalence and severity of MIH using Fisher's exact test. The patients with SCD, 4/18 (22%) taking daily antibiotics did not show a statistically significant greater prevalence of MIH compared to the control group, 24/63 (38%). There was no correlation between MIH and pneumonia, asthma, fever, flu, otitis media, breastfeeding, gender and birth weight. However, an association was noted between premature birth and MIH (p ≤ 0.05). No correlation was found between long-term antibiotic use and higher prevalence of MIH in the SCD group compared to the control group. However, MIH may be more severe in those with a history of long-term antibiotics.